test/jalview/ws2/actions/annotation/AnnotationJobTest.java

   1 package jalview.ws2.actions.annotation;
   2
   3 import static jalview.testutils.Matchers.matchesSequenceString;
   4 import static org.hamcrest.MatcherAssert.assertThat;
   5 import static org.hamcrest.Matchers.contains;
   6 import static org.hamcrest.Matchers.hasSize;
   7
   8 import java.util.List;
   9
  10 import org.testng.annotations.DataProvider;
  11 import org.testng.annotations.Test;
  12
  13 import jalview.datamodel.Alignment;
  14 import jalview.datamodel.Sequence;
  15 import jalview.datamodel.SequenceGroup;
  16
  17 public class AnnotationJobTest
  18 {
  19   @Test(groups = { "Functional" })
  20   public void testCreate_EqualLengthNoGapsSubmitGaps()
  21   {
  22     var alignment = new Alignment(new Sequence[] {
  23        new Sequence("test1", "ACACACACACA"),
  24        new Sequence("test2", "AVAVAVAVAVA"),
  25        new Sequence("test3", "AVWVAVWVAVW")
  26     });
  27     var annotJob = AnnotationJob.create(alignment, true, false, false, false, 0);
  28     assertThat(annotJob.getInputSequences(), contains(
  29             matchesSequenceString("ACACACACACA"),
  30             matchesSequenceString("AVAVAVAVAVA"),
  31             matchesSequenceString("AVWVAVWVAVW")
  32     ));
  33   }
  34
  35   @Test(groups = { "Functional" })
  36   public void testCreate_EqualLengthNoGapsNoSubmitGaps()
  37   {
  38     var alignment = new Alignment(new Sequence[] {
  39         new Sequence("test1", "ACACACACACA"),
  40         new Sequence("test2", "AVAVAVAVAVA"),
  41         new Sequence("test3", "AVWVAVWVAVW")
  42     });
  43     var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
  44     assertThat(annotJob.getInputSequences(), contains(
  45             matchesSequenceString("ACACACACACA"),
  46             matchesSequenceString("AVAVAVAVAVA"),
  47             matchesSequenceString("AVWVAVWVAVW")
  48     ));
  49   }
  50
  51   @Test(groups = { "Functional" })
  52   public void testCreate_UnequalLengthNoGapsNoSubmitGaps()
  53   {
  54     var alignment = new Alignment(new Sequence[] {
  55        new Sequence("test1", "ACACACACACA"),
  56        new Sequence("test2", "AVAVAVAVAVAVA"),
  57        new Sequence("test3", "AVWVAVWVAVWV")
  58     });
  59     var annotJob = AnnotationJob.create(alignment, true, false, false, false, 0);
  60     assertThat(annotJob.getInputSequences(), contains(
  61             matchesSequenceString("ACACACACACA"),
  62             matchesSequenceString("AVAVAVAVAVAVA"),
  63             matchesSequenceString("AVWVAVWVAVWV")
  64     ));
  65   }
  66
  67   @Test(groups = { "Functional" })
  68   public void testCreate_UnequalLengthNoGapsSubmitGaps()
  69   {
  70     var alignment = new Alignment(new Sequence[] {
  71         new Sequence("test1", "ACACACACACA"),
  72         new Sequence("test2", "AVAVAVAVAVAVA"),
  73         new Sequence("test3", "AVWVAVWVAVWV")
  74      });
  75      var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
  76      assertThat(annotJob.getInputSequences(), contains(
  77              matchesSequenceString("ACACACACACA"),
  78              matchesSequenceString("AVAVAVAVAVAVA"),
  79              matchesSequenceString("AVWVAVWVAVWV")
  80      ));
  81   }
  82
  83   @Test(groups = { "Functional" })
  84   public void testCreate_UnequalLengthNoGapsSubmitGapsRequireAligned()
  85   {
  86     var alignment = new Alignment(new Sequence[] {
  87         new Sequence("test1", "ACACACACACA"),
  88         new Sequence("test2", "AVAVAVAVAVAVA"),
  89         new Sequence("test3", "AVWVAVWVAVWV")
  90      });
  91      var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
  92      assertThat(annotJob.getInputSequences(), contains(
  93              matchesSequenceString("ACACACACACA--"),
  94              matchesSequenceString("AVAVAVAVAVAVA"),
  95              matchesSequenceString("AVWVAVWVAVWV-")
  96      ));
  97   }
  98
  99   @DataProvider
 100   public Object[] alignmentWithShortSequences()
 101   {
 102     return new Object[] {
 103         new Alignment(new Sequence[] {
 104             new Sequence("test1", "AAAAA"),
 105             new Sequence("test2", "ACAACAAACAAC"),
 106             new Sequence("test3", "ACA")
 107         }),
 108         new Alignment(new Sequence[] {
 109             new Sequence("test1", "----AAAAA---"),
 110             new Sequence("test2", "ACAACAAACAAC"),
 111             new Sequence("test3", "-----ACA----")
 112         }),
 113         new Alignment(new Sequence[] {
 114             new Sequence("test1", "--AAA---AA--"),
 115             new Sequence("test2", "ACAACAAACAAC"),
 116             new Sequence("test3", "-------ACA--")
 117         }),
 118     };
 119   }
 120
 121   @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
 122   public void testCreate_TooShortSequence_ShortSequenceRemoved(Alignment aln)
 123   {
 124     var annotJob = AnnotationJob.create(aln, true, false, false, false, 0);
 125     assertThat(annotJob.getInputSequences(), hasSize(1));
 126   }
 127
 128   @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
 129   public void testCreate_TooShortSequenceAndSubmitGaps_ShortSeqRemoved(Alignment aln)
 130   {
 131     var annotJob = AnnotationJob.create(aln, true, true, false, false, 0);
 132     assertThat(annotJob.getInputSequences(), hasSize(1));
 133   }
 134
 135   @Test(groups = { "Functional" }, dataProvider = "alignmentWithShortSequences")
 136   public void testCreate_TooShortSequenceAndRequireAligned_ShortSeqRemoved(Alignment aln)
 137   {
 138     var annotJob = AnnotationJob.create(aln, true, true, true, false, 0);
 139     assertThat(annotJob.getInputSequences(), hasSize(1));
 140   }
 141
 142   @Test(groups = { "Functional" })
 143   public void testCreate_EmptyColumnAndSubmitGaps_ColumnExtruded()
 144   {
 145     var alignment = new Alignment(new Sequence[] {
 146         new Sequence("test1", "ACA-ACAA--CACA"),
 147         new Sequence("test2", "AVA-AVAA-AVAVA"),
 148         new Sequence("test3", "AVAWAVAA-AVWVA")
 149     });
 150     var annotJob = AnnotationJob.create(alignment, true, true, false, false, 0);
 151     assertThat(annotJob.getInputSequences(), contains(
 152             matchesSequenceString("ACA-ACAA-CACA"),
 153             matchesSequenceString("AVA-AVAAAVAVA"),
 154             matchesSequenceString("AVAWAVAAAVWVA")
 155     ));
 156   }
 157
 158   @Test(groups = { "Functional" })
 159   public void testCreate_EmptyColumnAndRequireAligned_ColumnExtruded()
 160   {
 161     var alignment = new Alignment(new Sequence[] {
 162         new Sequence("test1", "ACA-ACAA--CACA"),
 163         new Sequence("test2", "AVA-AVAA-AVAVA"),
 164         new Sequence("test3", "AVAWAVAA-AVWVA")
 165     });
 166     var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
 167     assertThat(annotJob.getInputSequences(), contains(
 168             matchesSequenceString("ACA-ACAA-CACA"),
 169             matchesSequenceString("AVA-AVAAAVAVA"),
 170             matchesSequenceString("AVAWAVAAAVWVA")
 171     ));
 172   }
 173
 174   @Test(groups = { "Functional"} )
 175   public void testCreate_ContainsNonStandardAndNoFilterNonStandard_NonStandardRemain()
 176   {
 177     var alignment = new Alignment(new Sequence[] {
 178         new Sequence("test1", "ACACAOACACAC"),
 179         new Sequence("test2", "ABAVAVAVABAV")
 180     });
 181     var annotJob = AnnotationJob.create(alignment, true, true, true, false, 0);
 182     assertThat(annotJob.getInputSequences(), contains(
 183             matchesSequenceString("ACACAOACACAC"),
 184             matchesSequenceString("ABAVAVAVABAV")
 185     ));
 186   }
 187
 188   @Test(groups = { "Functional"} )
 189   public void testCreate_ContainsNonStandardAndFilterNonStandard_NonStandardToGap()
 190   {
 191     var alignment = new Alignment(new Sequence[] {
 192         new Sequence("test1", "ACACAOACACAC"),
 193         new Sequence("test2", "ABAVAVAVABAV")
 194     });
 195     var annotJob = AnnotationJob.create(alignment, true, true, true, true, 0);
 196     assertThat(annotJob.getInputSequences(), contains(
 197             matchesSequenceString("ACACA-ACACAC"),
 198             matchesSequenceString("A-AVAVAVA-AV")
 199     ));
 200   }
 201
 202   @DataProvider
 203   public Object[] alignmentWithNonStandardInColumns()
 204   {
 205     return new Object[] {
 206         new Alignment(new Sequence[] {
 207             new Sequence("test1", "A-AAAOAAAAAAAA"),
 208             new Sequence("test2", "ABAAA-AAAAAAAA")
 209         }),
 210         new Alignment(new Sequence[] {
 211             new Sequence("test1", "ABAAAOAAAAAAAA"),
 212             new Sequence("test2", "ABAAABAAAAAAAA")
 213         }),
 214         new Alignment(new Sequence[] {
 215             new Sequence("test1", "A-AAAOAAAAAAAA"),
 216             new Sequence("test2", "A-AAA-AAAAAAAA")
 217         })
 218     };
 219   }
 220
 221   @Test(groups = { "Functional" }, dataProvider = "alignmentWithNonStandardInColumns")
 222   public void testCreate_NonStandardInColumnsAndFilterNonStandard_ColumnsExtruded(Alignment aln)
 223   {
 224     var annotJob = AnnotationJob.create(aln, true, true, true, true, 0);
 225     assertThat(annotJob.getInputSequences(), contains(
 226             matchesSequenceString("AAAAAAAAAAAA"),
 227             matchesSequenceString("AAAAAAAAAAAA")
 228     ));
 229   }
 230
 231   @Test(groups = { "Functional" })
 232   public void testCreate_SequenceGroup_RegionSubmitted()
 233   {
 234     var group = new SequenceGroup(List.of(
 235        new Sequence("test1", "CCCCAAATAAATAAATCCC"),
 236        new Sequence("test2", "----AAATAAATAAAT---")
 237     ));
 238     group.setStartRes(4);
 239     group.setEndRes(15);
 240     var annotJob = AnnotationJob.create(group, true, false, false, false, 0);
 241     assertThat(annotJob.getInputSequences(), contains(
 242             matchesSequenceString("AAATAAATAAAT"),
 243             matchesSequenceString("AAATAAATAAAT")
 244     ));
 245   }
 246
 247   @Test(groups = { "Functional" })
 248   public void testCreate_RegionIncludingGaps_RegionSubmittedWithoutGaps()
 249   {
 250     var group = new SequenceGroup(List.of(
 251        new Sequence("test1", "CCCC-AAATAAATAAAT--CCC"),
 252        new Sequence("test2", "-----AAATAAATAAAT-----")
 253     ));
 254     group.setStartRes(4);
 255     group.setEndRes(18);
 256     var annotJob = AnnotationJob.create(group, true, false, false, false, 0);
 257     assertThat(annotJob.getInputSequences(), contains(
 258             matchesSequenceString("AAATAAATAAAT"),
 259             matchesSequenceString("AAATAAATAAAT")
 260     ));
 261   }
 262
 263   @Test(groups = { "Functional" })
 264   public void testCreate_RegionIncludingGapsAndSubmitGaps_RegionSubmittedGapsExtruded()
 265   {
 266     var group = new SequenceGroup(List.of(
 267        new Sequence("test1", "CCCC-AAATAAATAAAT--CCC"),
 268        new Sequence("test2", "-----AAATAAATAAAT-----")
 269     ));
 270     group.setStartRes(4);
 271     group.setEndRes(18);
 272     var annotJob = AnnotationJob.create(group, true, true, false, false, 0);
 273     assertThat(annotJob.getInputSequences(), contains(
 274             matchesSequenceString("AAATAAATAAAT"),
 275             matchesSequenceString("AAATAAATAAAT")
 276     ));
 277   }
 278 }